Figure 2

Functional coherence of random, functional, and dilute functional clusters. a) We show median functional coherence scores for random clusters, as well as clusters derived from functional site patterns. "PROSITE min" refers to the minimum cluster size for each PROSITE pattern cluster in Table 1 (derived from training sets used for existing FEATURE models [16]), while "PROSITE max" refers to the maximum size of each cluster. The PROSITE subsets were randomly sampled from the max PROSITE clusters, while the random clusters were randomly sampled from all Swiss-Prot proteins. The median functional coherence for the random clusters is clearly much lower than that for clusters derived from PROSITE. b) We plotted functional coherence as a function of percent signal. We decreased functional signal by randomly replacing members of the six "PROSITE min" clusters with either structurally similar proteins (left), or random proteins (right). Functional coherence decreases exponentially as the proportion of biological signal decreases.